Calcium in PDB 5k5s: Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain

The structure of Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain, PDB code: 5k5s was solved by Y.Geng, L.Mosyak, I.Kurinov, H.Zuo, E.Sturchler, T.C.Cheng, P.Subramanyam, A.P.Brown, S.C.Brennan, H.-C.Mun, M.Bush, Y.Chen, T.Nguyen, B.Cao, D.Chang, M.Quick, A.Conigrave, H.M.Colecraft, P.Mcdonald, Q.R.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.07 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.660, 127.450, 146.770, 90.00, 108.72, 90.00
R / Rfree (%)	21.1 / 22.2

The binding sites of Calcium atom in the Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain (pdb code 5k5s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain, PDB code: 5k5s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:53.2 occ:1.00 O A:LEU87 2.3 34.4 1.0 O A:SER84 2.7 41.5 1.0 O A:ILE81 2.7 33.8 1.0 O A:HOH828 2.9 25.4 1.0 O A:LEU88 3.3 38.2 1.0 C A:LEU87 3.6 35.0 1.0 O A:ASN82 3.6 39.5 1.0 C A:ILE81 3.8 34.4 1.0 C A:SER84 3.8 41.9 1.0 C A:LEU88 4.0 38.4 1.0 CA A:ASN82 4.0 33.9 1.0 C A:ASN82 4.0 39.3 1.0 O A:LEU91 4.1 41.0 1.0 N A:ASN82 4.3 33.2 1.0 N A:LEU88 4.4 33.0 1.0 CA A:PRO85 4.4 36.9 1.0 CB A:LEU88 4.4 33.5 1.0 CA A:LEU88 4.5 33.5 1.0 CG2 A:ILE81 4.5 26.3 1.0 N A:SER84 4.6 40.0 1.0 CA A:LEU87 4.6 29.2 1.0 N A:PRO85 4.6 37.6 1.0 C A:PRO85 4.6 39.8 1.0 O A:PRO85 4.7 39.1 1.0 N A:LEU87 4.7 31.2 1.0 CA A:SER84 4.7 38.9 1.0 N A:PRO89 4.7 35.0 1.0 CB A:LEU87 4.9 27.6 1.0 N A:SER83 4.9 37.0 1.0 CA A:PRO89 4.9 34.9 1.0 CA A:ILE81 5.0 25.9 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:56.6 occ:1.00 O A:HOH870 2.5 42.8 1.0 OG1 A:THR100 2.8 42.3 1.0 OG1 A:THR145 3.1 38.6 1.0 N A:THR145 3.2 23.8 1.0 CB A:ALA144 3.5 25.0 1.0 CB A:THR145 3.6 33.1 1.0 N A:PRO39 3.6 31.4 1.0 CD A:PRO39 3.6 31.4 1.0 CG A:PRO39 3.7 35.7 1.0 CG2 A:THR100 3.7 39.7 1.0 CB A:THR100 3.8 45.1 1.0 C A:PHE38 3.8 35.1 1.0 CA A:THR145 4.0 23.4 1.0 OH A:TYR167 4.0 35.2 1.0 CB A:PRO39 4.0 33.0 1.0 CA A:ALA144 4.0 24.3 1.0 CA A:PHE38 4.0 30.0 1.0 C A:ALA144 4.1 28.9 1.0 O A:LEU37 4.2 33.8 1.0 CA A:PRO39 4.2 32.2 1.0 N A:PHE38 4.3 31.1 1.0 C A:LEU37 4.3 33.8 1.0 O A:PHE38 4.4 35.2 1.0 N A:GLY146 4.7 23.3 1.0 OD1 A:ASN102 4.7 68.3 1.0 CG1 A:VAL149 4.8 27.6 1.0 C A:THR145 4.9 27.0 1.0 CG2 A:THR145 5.0 28.5 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:84.0 occ:1.00 O A:HOH822 2.2 21.6 1.0 O A:HOH879 2.3 69.1 1.0 OG A:SER302 3.4 47.7 1.0 N A:SER303 3.7 36.6 1.0 CA A:SER302 3.7 35.0 1.0 NH1 A:ARG66 3.8 15.8 1.0 CB A:SER302 4.0 37.6 1.0 CD1 A:LEU304 4.0 39.4 1.0 CE1 A:PHE42 4.0 48.1 1.0 OG A:SER303 4.2 41.8 1.0 C A:SER302 4.2 40.6 1.0 CZ A:PHE42 4.2 47.4 1.0 O A:HOH833 4.3 40.4 1.0 CD A:ARG66 4.3 22.1 1.0 O A:HOH807 4.7 28.8 1.0 CB A:SER303 4.7 36.4 1.0 CA A:SER303 4.7 35.6 1.0 OD1 A:ASN64 4.8 35.8 1.0 O A:HOH845 4.8 52.9 1.0 O A:SER301 4.8 39.5 1.0 N A:LEU304 4.8 35.1 1.0 CH2 A:TRP701 4.9 30.0 1.0 CZ A:ARG66 4.9 38.7 1.0 N A:SER302 4.9 35.1 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:0.5 occ:1.00 OD1 A:ASP234 2.2 75.0 1.0 O B:HOH898 2.7 50.3 1.0 O B:GLY557 2.9 78.3 1.0 O A:GLU231 2.9 63.8 1.0 CG A:ASP234 3.3 73.6 1.0 CA A:ASP234 3.9 59.3 1.0 CB A:ASP234 4.0 62.3 1.0 C B:GLY557 4.0 78.9 1.0 C A:GLU231 4.1 62.9 1.0 N A:ASP234 4.3 59.4 1.0 OD2 A:ASP234 4.3 79.9 1.0 O A:GLU232 4.8 64.6 1.0 CA A:GLU231 4.8 57.0 1.0 CA B:GLY557 4.9 75.9 1.0 N B:GLU558 5.0 74.8 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca712 b:0.6 occ:1.00 OD1 B:ASP234 2.2 69.0 1.0 O A:GLY557 2.6 75.3 1.0 O B:GLU231 2.8 58.3 1.0 O B:HOH900 3.1 48.8 1.0 CG B:ASP234 3.5 66.9 1.0 C A:GLY557 3.7 75.9 1.0 C B:GLU231 4.1 56.0 1.0 CA A:GLY557 4.3 72.9 1.0 CA B:ASP234 4.3 47.7 1.0 OD2 B:ASP234 4.3 73.2 1.0 CB B:ASP234 4.4 50.4 1.0 N B:ASP234 4.5 46.5 1.0 N A:GLU558 4.9 71.9 1.0 N B:GLU232 4.9 49.8 1.0 CA B:GLU231 5.0 51.1 1.0 CA B:GLU232 5.0 49.0 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca704 b:1.0 occ:1.00 O B:LEU87 2.2 0.1 1.0 O B:ILE81 2.5 90.2 1.0 O B:HOH801 2.5 68.3 1.0 O B:SER84 2.7 0.1 1.0 O B:LEU88 2.7 0.6 1.0 O B:ASN82 3.2 96.9 1.0 C B:LEU88 3.3 0.6 1.0 C B:LEU87 3.4 0.7 1.0 C B:ILE81 3.4 89.5 1.0 CA B:ASN82 3.6 89.5 1.0 C B:ASN82 3.6 97.0 1.0 N B:PRO89 3.8 0.2 1.0 N B:ASN82 3.9 88.0 1.0 C B:SER84 3.9 0.9 1.0 CA B:PRO89 3.9 0.9 1.0 CA B:LEU88 4.1 0.2 1.0 N B:LEU88 4.1 0.8 1.0 O B:LEU91 4.2 99.9 1.0 CG2 B:ILE81 4.4 84.6 1.0 CB B:LEU88 4.4 0.6 1.0 CA B:LEU87 4.5 0.9 1.0 N B:SER84 4.7 1.0 1.0 CA B:ILE81 4.7 82.1 1.0 N B:SER83 4.7 95.8 1.0 N B:LEU87 4.8 0.7 1.0 CA B:SER84 4.8 0.6 1.0 C B:PRO89 4.8 0.2 1.0 CA B:PRO85 4.8 0.7 1.0 N B:PRO85 4.8 0.0 1.0 CB B:LEU87 4.9 0.2 1.0 OD1 B:ASN82 4.9 99.9 1.0 CB B:ASN82 4.9 89.3 1.0 O B:PRO89 4.9 1.0 1.0 C B:SER83 5.0 0.5 1.0 CD B:PRO89 5.0 0.4 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca705 b:81.9 occ:1.00 O B:HOH804 2.4 33.0 1.0 OG1 B:THR100 2.9 35.4 1.0 N B:THR145 3.1 32.0 1.0 OG1 B:THR145 3.3 41.3 1.0 CB B:ALA144 3.4 37.6 1.0 CB B:THR145 3.5 35.6 1.0 CB B:THR100 3.8 36.9 1.0 CG2 B:THR100 3.8 30.8 1.0 CA B:THR145 3.9 31.8 1.0 CG B:PRO39 4.0 43.7 1.0 CD B:PRO39 4.0 39.5 1.0 N B:PRO39 4.0 38.5 1.0 CA B:ALA144 4.0 37.3 1.0 C B:ALA144 4.0 37.6 1.0 CB B:PRO39 4.2 40.1 1.0 C B:PHE38 4.3 41.3 1.0 N B:GLY146 4.3 33.4 1.0 OH B:TYR167 4.4 39.3 1.0 CG1 B:VAL149 4.4 32.2 1.0 OD1 B:ASN102 4.5 63.4 1.0 CA B:PHE38 4.5 36.3 1.0 CA B:PRO39 4.5 39.0 1.0 O B:LEU37 4.5 38.5 1.0 C B:THR145 4.6 38.1 1.0 N B:PHE38 4.7 35.6 1.0 C B:LEU37 4.7 38.9 1.0 CB B:VAL149 4.8 32.1 1.0 O B:PHE38 4.9 40.5 1.0 CG2 B:THR145 4.9 30.3 1.0 CA B:ASN102 5.0 41.3 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Active Form of Human Calcium-Sensing Receptor Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca706 b:0.8 occ:1.00 O B:HOH829 2.4 62.6 1.0 OG B:SER302 2.8 63.8 1.0 O B:HOH896 2.9 42.6 1.0 CD1 B:LEU304 3.6 56.9 1.0 CB B:SER302 3.6 55.6 1.0 O B:HOH815 3.6 50.1 1.0 CA B:SER302 3.9 52.9 1.0 CE1 B:PHE42 4.0 60.7 1.0 N B:SER303 4.3 54.0 1.0 CH2 B:TRP701 4.3 51.9 1.0 NH1 B:ARG66 4.3 47.0 1.0 CZ3 B:TRP701 4.5 51.3 1.0 CZ B:PHE42 4.5 60.6 1.0 OG B:SER303 4.5 67.2 1.0 C B:SER302 4.5 56.9 1.0 CD B:PRO274 4.6 44.4 1.0 CA B:GLY273 4.6 44.8 1.0 N B:GLY273 4.9 44.8 1.0 CG B:LEU304 4.9 56.6 1.0 N B:LEU304 4.9 52.7 1.0 CD1 B:PHE42 5.0 59.2 1.0 O B:ALA298 5.0 55.3 1.0

Y.Geng, L.Mosyak, I.Kurinov, H.Zuo, E.Sturchler, T.C.Cheng, P.Subramanyam, A.P.Brown, S.C.Brennan, H.C.Mun, M.Bush, Y.Chen, T.X.Nguyen, B.Cao, D.D.Chang, M.Quick, A.D.Conigrave, H.M.Colecraft, P.Mcdonald, Q.R.Fan. Structural Mechanism of Ligand Activation in Human Calcium-Sensing Receptor. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27434672
DOI: 10.7554/ELIFE.13662